JAL-3070 JAL-3066 JAL-3067 refactor annotation web service so client is passed sequen...

[jalview.git] / src / jalview / ws / jws2 / jabaws2 / AAConClient.java

diff --git a/src/jalview/ws/jws2/jabaws2/AAConClient.java b/src/jalview/ws/jws2/jabaws2/AAConClient.java
index f0a4b67..18b6ce1 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/AAConClient.java
+++ b/src/jalview/ws/jws2/jabaws2/AAConClient.java
@@ -20,10 +20,11 @@
  */
 package jalview.ws.jws2.jabaws2;
 
-import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.util.MessageManager;
-import jalview.ws.gui.AnnotationWsJob;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 
 import java.util.ArrayList;
@@ -64,13 +65,17 @@ public class AAConClient extends JabawsAnnotationInstance
   }
 
   @Override
-  List<AlignmentAnnotation> annotationFromScoreManager(
-          AnnotationWsJob running, AlignViewportI alignViewport,
-          boolean[] gapMap)
+  List<AlignmentAnnotation> annotationFromScoreManager(AlignmentI seqs,
+          Map<String, FeatureColourI> featureColours,
+          Map<String, FeatureMatcherSetI> featureFilters)
   {
+    return aacons_annotation(seqs.getWidth(), seqs, null);
+  }
 
+  private List<AlignmentAnnotation> aacons_annotation(int alWidth,
+          AlignmentI alignViewport, boolean[] gapMap)
+  {
     Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
-    int alWidth = alignViewport.getAlignment().getWidth();
     ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>();
     for (String score : scoremap.keySet())
     {
@@ -91,8 +96,9 @@ public class AAConClient extends JabawsAnnotationInstance
         }
         else
         {
-          createAnnotationRowsForScores(alignViewport, gapMap, ourAnnot,
-                  getCalcId(), alWidth, scr);
+          createAnnotationRowsForScores(alignViewport, null, ourAnnot,
+                  getCalcId(),
+                  scr.getScores().size(), scr);
         }
       }
     }